Yea I can see the idea as a good one but I don't think it would help much. If someone wants to steal a quilt they are going to steal the quilt and that will be the end of it and probably the last time it is seen. Quilts aren't like dogs that accidentally walk off and get lost :( And unless every quilt show starts to search for microchips there is really little good that a microchip would do. Nothing stops the theft.
I think the best way to protect yourself from theft would be to insure your quilt. Not the same at all. Money doesn't bring back the hours and hours that you spent on a quilt. But it is better than nothing.